Mercurial > repos > fgiacomoni > hr2
comparison hr2_manager.pl @ 2:23970530a518 draft
master branch Updating with tag :CI_COMMIT_TAG - - Fxx
| author | fgiacomoni |
|---|---|
| date | Tue, 17 Jan 2023 10:31:32 +0000 |
| parents | e2cbcf6fa22e |
| children | 78afd7f439f3 |
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| 1:e2cbcf6fa22e | 2:23970530a518 |
|---|---|
| 158 print "Current MZ send to HR\n" if $verbose == 3 ; | 158 print "Current MZ send to HR\n" if $verbose == 3 ; |
| 159 print Dumper $exact_mass if $verbose == 3 ; | 159 print Dumper $exact_mass if $verbose == 3 ; |
| 160 ## build exe line | 160 ## build exe line |
| 161 my $ohr_exe = lib::hr->new() ; | 161 my $ohr_exe = lib::hr->new() ; |
| 162 my $hr_cmd = $ohr_exe->config_hr_exe( \$CONF->{'HR2_EXE'}, \$tolerance, $exact_mass, \$has_golden_rules, \$atomsCurrentConf ) ; | 162 my $hr_cmd = $ohr_exe->config_hr_exe( \$CONF->{'HR2_EXE'}, \$tolerance, $exact_mass, \$has_golden_rules, \$atomsCurrentConf ) ; |
| 163 print "$hr_cmd\n" if $verbose == 3 ; | 163 print "$$hr_cmd\n" if $verbose == 3 ; |
| 164 push(@{$hr_cmds}, $$hr_cmd) ; | 164 push(@{$hr_cmds}, $$hr_cmd) ; |
| 165 } | 165 } |
| 166 | 166 |
| 167 ## MultiThreading execution of Hr : | 167 ## MultiThreading execution of Hr : |
| 168 my $threads = lib::hr->new() ; | 168 my $threads = lib::hr->new() ; |
| 190 my $oHtml = lib::hr::new() ; | 190 my $oHtml = lib::hr::new() ; |
| 191 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; | 191 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; |
| 192 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids, $parsed_results ) ; | 192 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids, $parsed_results ) ; |
| 193 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $parsed_results) ; | 193 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $parsed_results) ; |
| 194 | 194 |
| 195 print Dumper $tbody_object ; | 195 #print Dumper $tbody_object ; |
| 196 | 196 |
| 197 my $html_file = $binPath.'/'.$CONF->{'HTML_TEMPLATE'} ; | 197 my $html_file = $binPath.'/'.$CONF->{'HTML_TEMPLATE'} ; |
| 198 my $output = $oHtml->write_html_skel(\$output_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $html_file, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; | 198 my $output = $oHtml->write_html_skel(\$output_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $html_file, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; |
| 199 | 199 |
| 200 } ## END IF | 200 } ## END IF |
| 204 | 204 |
| 205 if ( ( defined $output_csv ) and ( defined $parsed_results ) ) { | 205 if ( ( defined $output_csv ) and ( defined $parsed_results ) ) { |
| 206 # produce a csv based on METLIN format | 206 # produce a csv based on METLIN format |
| 207 my $ocsv = lib::hr::new() ; | 207 my $ocsv = lib::hr::new() ; |
| 208 if (defined $input_file) { | 208 if (defined $input_file) { |
| 209 my $lm_matrix = undef ; | 209 my $hr_matrix = undef ; |
| 210 if ( ( defined $line_header ) and ( $line_header == 1 ) ) { $lm_matrix = $ocsv->set_hr_matrix_object('hr2', $masses, $parsed_results ) ; } | 210 if ( ( defined $line_header ) and ( $line_header == 1 ) ) { $hr_matrix = $ocsv->set_hr_matrix_object('hr2', $masses, $parsed_results ) ; } |
| 211 elsif ( ( defined $line_header ) and ( $line_header == 0 ) ) { $lm_matrix = $ocsv->set_hr_matrix_object(undef, $masses, $parsed_results ) ; } | 211 elsif ( ( defined $line_header ) and ( $line_header == 0 ) ) { $hr_matrix = $ocsv->set_hr_matrix_object(undef, $masses, $parsed_results ) ; } |
| 212 $lm_matrix = $ocsv->add_hr_matrix_to_input_matrix($complete_rows, $lm_matrix) ; | 212 |
| 213 $ocsv->write_csv_skel(\$output_csv, $lm_matrix) ; | 213 $hr_matrix = $ocsv->add_hr_matrix_to_input_matrix($complete_rows, $hr_matrix) ; |
| 214 $ocsv->write_csv_skel(\$output_csv, $hr_matrix) ; | |
| 214 } | 215 } |
| 215 elsif (defined $mass) { | 216 elsif (defined $mass) { |
| 216 $ocsv->write_csv_one_mass($masses, $ids, $parsed_results, $output_csv) ; | 217 $ocsv->write_csv_one_mass($masses, $ids, $parsed_results, $output_csv) ; |
| 217 } | 218 } |
| 218 } ## END IF | 219 } ## END IF |
| 242 print Dumper $masses ; | 243 print Dumper $masses ; |
| 243 print "-- Inputs initiales ids :\n" ; | 244 print "-- Inputs initiales ids :\n" ; |
| 244 print Dumper $ids ; | 245 print Dumper $ids ; |
| 245 print "-- Hr_Cmds :\n" ; | 246 print "-- Hr_Cmds :\n" ; |
| 246 print Dumper $hr_cmds ; | 247 print Dumper $hr_cmds ; |
| 247 print "-- Hr_Results :\n" ; | 248 # print "-- Hr_Results :\n" ; |
| 248 # print Dumper $results ; | 249 # print Dumper $results ; |
| 249 print "-- Hr_parsed Results :\n" ; | 250 # print "-- Hr_parsed Results :\n" ; |
| 250 print Dumper $parsed_results ; | 251 # print Dumper $parsed_results ; |
| 251 | 252 |
| 252 my $nb_results = scalar (@{$results}) ; | 253 my $nb_results = scalar (@{$results}) ; |
| 253 print "-- Hr_Results return : $nb_results\n" ; | 254 print "-- Hr_Results return : $nb_results\n" ; |
| 254 } | 255 } |
| 255 | 256 |